5.integration Design a Binding Site

Design a Binding Site (Module 5: The Explorer). Key concept: Integration exercise. Survey a target ligand and identify the chemical features a pocket must complement.

• Survey a target ligand and identify the chemical features a pocket must complement
• Carve a pocket by replacing surface residues with smaller ones
• Line the pocket with residues that complement the ligand chemically
• Assess the result through a simplified docking evaluation
• Combine everything from 5.1 to 5.5 into one design workflow